Georgia voters line up during early voting at a polling location in Decatur, Georgia, on 22 October.
Photograph: Tami Chappell/EPA

A federal judge has ordered election officials in Georgia to stop throwing out absentee ballots solely because of a suspected signature mismatch. The decision was a victory for voting rights activists who feared the practice could disenfranchise thousands of eligible voters.

The temporary restraining order on Wednesday amounted to a striking rebuke of Brian Kemp, the controversial Georgia state elections chief who is also running for governor in one of the most closely fought and closely watched races of the midterms.

Judge Leigh Martin May agreed with the plaintiffs, led by the American Civil Liberties Union, that rejecting absentee ballots without notifying voters or offering them a chance to resolve any discrepancy was a violation of their rights of equal protection and due process under the fourteenth amendment.

She ordered authorities to include the ballots in the provisional vote tally and give affected voters up to three days after the 6 November election to prove their eligibility.

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May also firmly rejected the state’s argument that the arrangement would be overly burdensome so close to election day and risked compromising the overall integrity of the process. “The Court does not understand how assuring that all eligible voters are permitted to vote undermines integrity of the election process,” she wrote. “To the contrary, it strengthens it.”

The rejections have been particularly alarming in Gwinnett county, in the northern Atlanta suburbs, where election officials have tossed close to 1 in 10 absentee ballots. Voting rights activists point out that the rejections have disproportionately affected black and Asian voters in a fast-growing county that has shifted from majority white to majority non-white in the past 15 years.

The ballot rejections in Gwinnett account for one-third of the statewide total.

Kemp, a pro-Trump conservative, has thrown hundreds of thousands of people off voter registration lists and fought for a 2017 “exact match” law empowering voting officials to reject registration applications for as little as a missing hyphen.

This month, it emerged that Kemp’s office had put 53,000 largely minority voter registrations on hold because of exact-match concerns. When the story made national headlines, Kemp insisted that anyone on the list was still eligible to cast a ballot as long as he or she turned up at the polls on election day with a valid government-issued ID.

The voting rights controversy has cast a long shadow over the gubernatorial race pitting Kemp against Stacey Abrams, a former minority leader in the Georgia state house who has also campaigned to register hundreds of thousands of new voters, particularly minority voters who are rapidly changing the demographic and political complexion of a once solid-red southern state.

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Voting rights surfaced almost immediately in a Tuesday night gubernatorial debate, as Kemp accused Abrams without evidence of encouraging non-citizens, including undocumented immigrants, to vote. Abrams, in return, accused Kemp of using scare tactics as well as suppression techniques to keep eligible voters at home.

Kemp has staunchly resisted calls to step down as Georgia’s secretary of state so he does not end up overseeing the vote count in his own race, and on Tuesday he said he would not recuse himself even in the event of a recount.

Polls show the two candidates neck and neck.

May’s order covers only part of the controversy over rejected absentee ballots, because mismatched signatures are only one of the issues at hand. Many ballots in Gwinnett county and elsewhere are being tossed because the information is incomplete, because the signature is missing, or because the voter was found to be ineligible.

May’s court has received a brief from the plaintiffs urging remedial action on the other issues, but she said she needed to hear from the government before ruling on those.